Profiling Calcium-Dependent Gene Expression and Identifying Functional Diversity in Human Islet Cell Types

Abstract

All pancreatic endocrine cells depend on cytosolic calcium signaling to trigger the secretion of glucoregulatory hormones, and rapidly regulate transcription of genes important for islet function and the response to stimuli. In order to profile calcium-regulated genes in islet cell types, we performed single cell RNA sequencing on intact non-diabetic human islets (3 donors) exposed to conditions designed to acutely induce or inhibit intracellular calcium signaling for 1 hour: 1) a low glucose dose of 2.8 mmol/L, 2) stimulatory 25 mmol/L glucose and 40 mmol/L KCl, and 3) 25 mmol/L glucose, 40 mmol/L KCl, and 5 mmol/L inhibitory calcium chelator EGTA. After downstream filtering and quality control, we obtained a robust dataset of 68,650 cells, which included 59,373 alpha, beta, delta and PP cells. By comparing the transcriptomes from stimulatory and inhibitory conditions, we identified 38 calcium-regulated genes across the islet, including 15 specific to alpha cells and 10 specific to beta cells. We also observed distinct clusters expressing both insulin and glucagon, or insulin and somatostatin, and these clusters express a unique set of 14 calcium-regulated genes. In beta cell subtypes that expressed the greatest number of calcium-regulated genes, we identified the gene PCDH7 as a novel marker of beta cells with an enhanced glucose-stimulated insulin secretory function. We share this large human islet single cell transcriptome dataset as an accessible, user-friendly web tool to easily generate plots and query gene expression in single human islet cells.